Make obitag able to use the taxonomic path included in reference database as taxonomy

cmd/obitools/obitag/main.go

@@ -47,12 +47,27 @@ func main() {
 	obiconvert.OpenSequenceDataErrorMessage(args, err)
 
 	taxo := obitax.DefaultTaxonomy()
+
+	references := obitag.CLIRefDB()
+
+	if references == nil {
+		log.Panicln("No loaded reference database")
+	}
+
+	if taxo == nil {
+		taxo, err = references.ExtractTaxonomy(nil)
+
+		if err != nil {
+			log.Fatalf("No taxonomy specified or extractable from reference database: %v", err)
+		}
+
+		taxo.SetAsDefault()
+	}
+
 	if taxo == nil {
 		log.Panicln("No loaded taxonomy")
 	}
 
-	references := obitag.CLIRefDB()
-
 	var identified obiiter.IBioSequence
 
 	if obitag.CLIGeometricMode() {

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "2452aef"
+var _Commit = "0df082d"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obitag/options.go

@@ -6,7 +6,6 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -43,7 +42,6 @@ func TagOptionSet(options *getoptions.GetOpt) {
 // the obiuniq command
 func OptionSet(options *getoptions.GetOpt) {
 	obiconvert.OptionSet(options)
-	obioptions.LoadTaxonomyOptionSet(options, true, false)
 	TagOptionSet(options)
 }